Khanom the district is located in the north of the province. To the west is Surat Thani Province, while to the north and east is the Gulf of Thailand. Neighboring districts are (from the south clockwise) Sichon of Nakhon Si Thammarat and Don Sak of Surat Thani.
Most of the coast line of district will be protected as part of the Khanom Beach- South Sea island National marine park, which is currently in process of creation. The coast of the district consists of a series of beaches nestled among the limestone and shale mountains of northern Nakhon Si Thammarat mountain range. Nai Plao Beach is the most popular of these beaches. Several caves are found in the hills, the most famous one is Khao Wang Thong cave. The major hills within the districts are Khao Luang (814 m), Khao Phlao and Khao Dat Fa (732 m) at the southeastern boundary to Sichon and Khao Chai Son (535 m) adjacent Khanom town at the Khanom Bay, the mouth of Khlong Khanom.
The main road is Highway 401, which passes through the southwestern part of the district. Route 4014 connects the district center which that highway, while 4142 connects the center with Don Sak